Gravel excavation often bears conflicts with the use of drinking water as under-water-table mining can directly impact groundwater quality downstream of the open gravel pit lake due to exposure of the groundwater aquifer to the atmosphere and to human activities. To assess this potential impact of GPLs on groundwater, we assessed the mass balance for nitrate (NO₃) and phosphate (PO₄) and whole-ecosystem metabolism of five post-excavation GPLs in Austria. GPLs differed in both age and residence time of lake water. We found that GPLs significantly reduced the concentration of NO₃ and PO₄ as groundwater passes through the lake ecosystem, which in most cases acted as a net sink for these nutrients. Groundwater-derived nutrients enhanced both epilithic and pelagic net primary production in the GPLs, which ultimately leads to biomass accrual. Our data also suggest that this biomass accrual may induce, at least in part, clogging of the GPLs and their successive hydrodynamic isolation from the adjacent groundwater. Despite continuous biomass build-up and elevated concentrations of dissolved organic carbon (DOC) in the lake water compared to the inflowing groundwater, DOC export into the outflowing groundwater remained low. Our data suggest that GPLs could contribute to groundwater amelioration where agricultural land use increases nutrient concentrations in the groundwater given a proper management of these man-made ecosystems.